Magnesium in PDB 7knz: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site, PDB code: 7knz was solved by S.Saran, D.A.R.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.91 / 2.28
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.12, 231.21, 200.12, 90, 90, 90
R / Rfree (%) 18 / 21.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site (pdb code 7knz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site, PDB code: 7knz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 7knz

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Magnesium binding site 1 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:35.2
occ:1.00
 O A:HOH406 2.0 29.0 1.0
OD2 A:ASP227 2.2 28.1 1.0
O A:HOH453 2.3 31.2 1.0
CG A:ASP227 2.8 27.1 1.0
OD1 A:ASP227 3.0 33.0 1.0
CB A:ASP227 4.1 26.4 1.0
O A:HOH421 4.4 24.1 1.0
O A:HOH514 4.8 33.9 1.0

Magnesium binding site 2 out of 10 in 7knz

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Magnesium binding site 2 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:45.9
occ:1.00
 O A:HOH537 2.1 41.4 1.0
O A:LYS71 3.7 25.8 1.0
O A:GLY72 4.2 24.7 1.0
CA A:GLY72 4.3 24.4 1.0
C A:GLY72 4.4 28.1 1.0
CG2 A:THR73 4.7 24.6 1.0
C A:LYS71 4.8 27.6 1.0

Magnesium binding site 3 out of 10 in 7knz

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Magnesium binding site 3 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:33.0
occ:1.00
 OD2 B:ASP227 2.0 30.5 1.0
O B:HOH469 2.1 38.0 1.0
CG B:ASP227 3.0 26.3 1.0
OD1 B:ASP227 3.4 34.4 1.0
O B:HOH444 3.9 26.5 1.0
CB B:ASP227 4.3 28.2 1.0
O B:HOH482 4.4 37.2 1.0

Magnesium binding site 4 out of 10 in 7knz

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Magnesium binding site 4 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:38.8
occ:1.00
 O B:HOH414 3.0 27.6 1.0
N01 B:3VN301 3.3 28.2 1.0
CB B:ALA88 3.5 23.2 1.0
C11 B:3VN301 3.6 28.4 1.0
C06 B:3VN301 3.7 26.4 1.0
C02 B:3VN301 3.8 32.9 1.0
OG B:SER83 3.9 25.9 1.0
NE2 B:HIS56 3.9 38.4 1.0
MG C:MG302 4.3 56.9 1.0
CB B:ALA85 4.5 25.9 1.0
CE1 B:HIS56 4.7 37.0 1.0
C15 B:3VN301 4.7 29.0 1.0
C07 B:3VN301 4.8 24.9 1.0
O C:ALA52 4.8 31.5 1.0
C12 B:3VN301 4.9 27.9 1.0
CD2 B:HIS56 5.0 34.9 1.0
CA B:ALA88 5.0 28.8 1.0

Magnesium binding site 5 out of 10 in 7knz

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Magnesium binding site 5 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:38.6
occ:1.00
 O C:GLY203 3.2 29.2 1.0
O C:LEU199 3.2 28.2 1.0
NZ C:LYS204 3.3 43.9 1.0
OH C:TYR230 3.8 46.3 1.0
CA C:GLY202 4.0 28.7 1.0
C C:GLY202 4.1 26.6 1.0
CE C:LYS204 4.1 33.1 1.0
O C:HOH538 4.2 42.1 1.0
CD C:LYS204 4.2 31.6 1.0
C C:GLY203 4.3 25.3 1.0
O C:ALA225 4.3 31.3 1.0
C C:LEU199 4.3 25.9 1.0
O C:GLY202 4.3 31.1 1.0
CD2 C:LEU226 4.4 26.6 1.0
N C:GLY202 4.4 25.4 1.0
N C:GLY203 4.5 27.7 1.0
O C:HOH442 4.6 44.5 1.0
CE1 C:TYR230 4.8 36.3 1.0
CZ C:TYR230 4.8 44.6 1.0
CA C:LEU226 4.8 31.3 1.0
C C:ALA225 4.9 30.5 1.0
CA C:LEU199 4.9 24.7 1.0

Magnesium binding site 6 out of 10 in 7knz

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Magnesium binding site 6 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:56.9
occ:1.00
 O B:HOH536 2.3 47.0 1.0
CD2 C:HIS56 3.7 34.7 1.0
CD2 B:HIS56 3.7 34.9 1.0
C1 C:EDO306 3.8 31.4 1.0
NE2 C:HIS56 3.9 32.2 1.0
C2 C:EDO306 3.9 35.4 1.0
O C:HOH527 3.9 37.3 1.0
O B:HOH402 4.0 43.9 1.0
NE2 B:HIS56 4.0 38.4 1.0
MG B:MG303 4.3 38.8 1.0
O B:HOH539 4.4 47.1 1.0
C06 B:3VN301 4.4 26.4 1.0
C15 B:3VN301 4.6 29.0 1.0
O1 C:EDO306 4.7 29.5 1.0
CG C:HIS56 5.0 40.5 1.0

Magnesium binding site 7 out of 10 in 7knz

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Magnesium binding site 7 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:41.4
occ:1.00
 OD1 D:ASP40 2.2 29.4 1.0
O D:HOH518 2.9 37.2 1.0
CG D:ASP40 3.4 29.6 1.0
NE2 D:HIS223 3.7 26.6 1.0
OD2 D:ASP40 4.0 30.4 1.0
CE1 D:HIS223 4.0 29.1 1.0
O D:GLY38 4.2 33.8 1.0
CB D:ASP40 4.5 27.9 1.0
CD2 D:HIS223 4.7 27.4 1.0
CA D:ASP40 4.8 24.9 1.0
O D:HOH528 4.9 35.3 1.0

Magnesium binding site 8 out of 10 in 7knz

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Magnesium binding site 8 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:51.1
occ:1.00
 CG2 A:THR55 4.0 28.8 1.0
CG D:HIS87 4.2 42.3 1.0
ND1 D:HIS87 4.3 41.3 1.0
CD2 D:HIS87 4.3 38.1 1.0
NH1 A:ARG272 4.4 33.9 1.0
CE1 D:HIS87 4.4 32.3 1.0
NE2 D:HIS87 4.4 39.3 1.0
CZ A:ARG272 4.6 31.2 1.0
CB D:HIS87 4.7 36.4 1.0
NH2 A:ARG272 4.8 35.8 1.0

Magnesium binding site 9 out of 10 in 7knz

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Magnesium binding site 9 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:48.0
occ:1.00
 O C:HOH534 2.1 53.0 1.0
O E:HOH516 2.3 53.5 1.0
O E:HOH463 3.1 38.7 1.0
O E:HOH426 3.2 41.3 1.0
O E:TYR261 3.5 30.1 1.0
O C:HOH502 3.8 42.8 1.0
CA C:GLU36 4.0 38.0 1.0
CG C:GLU36 4.3 39.7 1.0
O E:LEU262 4.3 31.7 1.0
O C:ILE35 4.4 38.0 1.0
CB C:GLU36 4.4 33.7 1.0
CZ E:TYR261 4.6 40.2 1.0
C E:TYR261 4.6 32.9 1.0
N E:GLY264 4.7 31.4 1.0
CA E:GLY264 4.7 31.8 1.0
CE1 E:TYR261 4.8 35.5 1.0
C E:LEU262 4.8 33.0 1.0
CA E:LEU262 4.8 28.3 1.0
C C:GLU36 4.8 36.8 1.0
N C:GLU36 4.8 34.5 1.0
O C:GLU36 4.8 39.0 1.0
CE2 E:TYR261 4.9 38.7 1.0
C C:ILE35 4.9 33.8 1.0
OH E:TYR261 4.9 44.9 1.0

Magnesium binding site 10 out of 10 in 7knz

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Magnesium binding site 10 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:52.8
occ:1.00
 O E:HOH534 2.4 59.6 1.0
CG E:HIS87 3.9 41.6 1.0
CD2 E:HIS87 4.0 41.2 1.0
ND1 E:HIS87 4.2 41.8 1.0
NE2 E:HIS87 4.3 34.9 1.0
CG2 F:THR55 4.3 31.1 1.0
CB E:HIS87 4.4 36.7 1.0
CE1 E:HIS87 4.4 36.7 1.0
NH1 F:ARG272 4.5 33.9 1.0
CZ F:ARG272 4.5 35.5 1.0
NH2 F:ARG272 4.6 34.5 1.0
NE F:ARG272 4.8 35.6 1.0

Reference:

S.Saran, M.Majdi Yazdi, I.Chung, D.A.R.Sanders. The Allosteric Site Residue, E88 Interacts with the Inhibitors to Transmit the Allosteric Inhibition Signals in Cj.Dhdps By Forming A Hydrogen Bond. To Be Published.
Page generated: Thu Nov 25 10:02:03 2021

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